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EDC3 enhancer of mRNA decapping 3 [ Homo sapiens (human) ]

Gene ID: 80153, updated on 5-Mar-2024

Summary

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Official Symbol
EDC3provided by HGNC
Official Full Name
enhancer of mRNA decapping 3provided by HGNC
Primary source
HGNC:HGNC:26114
See related
Ensembl:ENSG00000179151 MIM:609842; AllianceGenome:HGNC:26114
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
YJDC; LSM16; MRT50; YJEFN2; hYjeF_N2-15q23
Summary
This gene encodes a protein that is important in mRNA degradation. The encoded protein is a component of a decapping complex that promotes efficient removal of the monomethylguanosine (m7G) cap from mRNAs, as part of the 5' to 3' mRNA decay pathway. Mutations in this gene have been identified in human patients with an autosomal recessive form of intellectual disability. [provided by RefSeq, May 2017]
Expression
Ubiquitous expression in testis (RPKM 14.2), ovary (RPKM 7.5) and 25 other tissues See more
Orthologs
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Genomic context

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Location:
15q24.1
Exon count:
12
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 15 NC_000015.10 (74630558..74696024, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 15 NC_060939.1 (72500459..72565921, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 15 NC_000015.9 (74922899..74988365, complement)

Chromosome 15 - NC_000015.10Genomic Context describing neighboring genes Neighboring gene AT-rich interaction domain 3B Neighboring gene uncharacterized LOC124903527 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:74880397-74881182 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:74881183-74881968 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:74886857-74887357 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:74889350-74889850 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:74890466-74891354 Neighboring gene uncharacterized LOC102723750 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6653 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6654 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:74908320-74908931 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:74908932-74909542 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9785 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:74921666-74922166 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9786 Neighboring gene CDC like kinase 3 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9787 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9788 Neighboring gene CYP1A1 5' regulatory region Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr15:75021499-75022227 Neighboring gene cytochrome P450 family 1 subfamily A member 1 Neighboring gene CYP1A2 5' regulatory region Neighboring gene cytochrome P450 family 1 subfamily A member 2

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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Related articles in PubMed

  1. Integrative bioinformatics analysis characterizing the role of EDC3 in mRNA decay and its association to intellectual disability. Scheller U, et al. BMC Med Genomics, 2018 Apr 23. PMID 29685133, Free PMC Article
  2. Structure of a Human 4E-T/DDX6/CNOT1 Complex Reveals the Different Interplay of DDX6-Binding Proteins with the CCR4-NOT Complex. Ozgur S, et al. Cell Rep, 2015 Oct 27. PMID 26489469
  3. mRNA decapping factors and the exonuclease Xrn2 function in widespread premature termination of RNA polymerase II transcription. Brannan K, et al. Mol Cell, 2012 May 11. PMID 22483619, Free PMC Article
  4. Mutations in DCPS and EDC3 in autosomal recessive intellectual disability indicate a crucial role for mRNA decapping in neurodevelopment. Ahmed I, et al. Hum Mol Genet, 2015 Jun 1. PMID 25701870, Free PMC Article
  5. Crystal structure of human Edc3 and its functional implications. Ling SH, et al. Mol Cell Biol, 2008 Oct. PMID 18678652, Free PMC Article

See all (97) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. EDC3 might be preferentially involved in the degradation of long coding and non-coding RNAs
    Title: Integrative bioinformatics analysis characterizing the role of EDC3 in mRNA decay and its association to intellectual disability.
  2. In vitro decapping assays showed that altered EDC3 is unable to enhance DCP2 decapping at low concentrations and even inhibits DCP2 decapping at high concentration.
    Title: Mutations in DCPS and EDC3 in autosomal recessive intellectual disability indicate a crucial role for mRNA decapping in neurodevelopment.
  3. Structural basis for the mutually exclusive anchoring of P body components EDC3 and Tral to the DEAD box protein DDX6/Me31B.
    Title: Structural basis for the mutually exclusive anchoring of P body components EDC3 and Tral to the DEAD box protein DDX6/Me31B.
  4. The dimerization interface of Edc3 is highly conserved in eukaryotes despite the overall low sequence homology across species; structure-based site-directed mutagenesis revealed dimerization is required for efficient RNA binding, P-body formation
    Title: Crystal structure of human Edc3 and its functional implications.
  5. The modular architecture enables EDC3 to interact with multiple components of the decapping machinery, including DCP1, DCP2, and Me31B.
    Title: A divergent Sm fold in EDC3 proteins mediates DCP1 binding and P-body targeting.
Submit: New GeneRIF Correction

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Associated conditions

Description Tests
Intellectual disability, autosomal recessive 50
MedGen: C4225319 OMIM: 616460 GeneReviews: Not available
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EBI GWAS Catalog

Description
Genome-wide meta-analysis identifies regions on 7p21 (AHR) and 15q24 (CYP1A2) as determinants of habitual caffeine consumption.
EBI GWAS Catalog

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

Pathways from PubChem

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Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Clone Names

  • FLJ21128, FLJ31777

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables identical protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables mRNA binding IBA
Inferred from Biological aspect of Ancestor
more info
  
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
Process Evidence Code Pubs
involved_in P-body assembly IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in deadenylation-independent decapping of nuclear-transcribed mRNA IBA
Inferred from Biological aspect of Ancestor
more info
  
Component Evidence Code Pubs
is_active_in P-body IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in cytoplasmic ribonucleoprotein granule IDA
Inferred from Direct Assay
more info
  
located_in cytosol TAS
Traceable Author Statement
more info
  
located_in membrane HDA PubMed 

General protein information

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Preferred Names
enhancer of mRNA-decapping protein 3
Names
LSM16 homolog (EDC3, S. cerevisiae)
enhancer of mRNA decapping 3 homolog
yjeF N-terminal domain-containing protein 2
yjeF domain containing
yjeF domain-containing protein 1

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

  1. NG_054910.1 RefSeqGene

    Range
    5022..70488
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001142443.3 → NP_001135915.1  enhancer of mRNA-decapping protein 3 isoform 1

    See identical proteins and their annotated locations for NP_001135915.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longest transcript and encodes the longer isoform (1). Variants 1-4 encode the same isoform (1).
    Source sequence(s)
    AC091230, AL133447, BC021271, BM999594, CA440205
    Consensus CDS
    CCDS10267.1
    UniProtKB/Swiss-Prot
    B3KPH0, D3DW61, Q96F86, Q9H797
    Related
    ENSP00000401343.3, ENST00000426797.7
    Conserved Domains (4) summary
    cd01737
    Location:2 → 66
    LSm16_N; Like-Sm protein 16, N-terminal domain
    pfam03853
    Location:302 → 455
    YjeF_N; YjeF-related protein N-terminus
    pfam09532
    Location:199 → 300
    FDF; FDF domain
    pfam16598
    Location:104 → 197
    Edc3_linker; Linker region of enhancer of mRNA-decapping protein 3

  2. NM_001142444.3 → NP_001135916.1  enhancer of mRNA-decapping protein 3 isoform 1

    See identical proteins and their annotated locations for NP_001135916.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) differs in the 5' UTR compared to variant 1. Variants 1-4 encode the same isoform (1).
    Source sequence(s)
    AF193058, AK024781, AL133447, CA440205, DA168050, DB007958
    Consensus CDS
    CCDS10267.1
    UniProtKB/Swiss-Prot
    B3KPH0, D3DW61, Q96F86, Q9H797
    Related
    ENSP00000455580.1, ENST00000568176.5
    Conserved Domains (4) summary
    cd01737
    Location:2 → 66
    LSm16_N; Like-Sm protein 16, N-terminal domain
    pfam03853
    Location:302 → 455
    YjeF_N; YjeF-related protein N-terminus
    pfam09532
    Location:199 → 300
    FDF; FDF domain
    pfam16598
    Location:104 → 197
    Edc3_linker; Linker region of enhancer of mRNA-decapping protein 3

  3. NM_001351378.2 → NP_001338307.1  enhancer of mRNA-decapping protein 3 isoform 1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) differs in the 5' UTR compared to variant 1. Variants 1-4 encode the same isoform (1).
    Source sequence(s)
    AC091230, AC100835, BC011534
    Consensus CDS
    CCDS10267.1
    UniProtKB/Swiss-Prot
    B3KPH0, D3DW61, Q96F86, Q9H797
    Related
    ENSP00000497737.1, ENST00000647659.1
    Conserved Domains (4) summary
    cd01737
    Location:2 → 66
    LSm16_N; Like-Sm protein 16, N-terminal domain
    pfam03853
    Location:302 → 455
    YjeF_N; YjeF-related protein N-terminus
    pfam09532
    Location:199 → 300
    FDF; FDF domain
    pfam16598
    Location:104 → 197
    Edc3_linker; Linker region of enhancer of mRNA-decapping protein 3

  4. NM_001351379.2 → NP_001338308.1  enhancer of mRNA-decapping protein 3 isoform 2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (5) differs in the 5' UTR and initiates translation at a downstream start codon compared to variant 1. The encoded isoform (2) has a shorter N-terminus than isoform 1.
    Source sequence(s)
    AC091230, AC100835, BC011534
    Conserved Domains (3) summary
    pfam03853
    Location:157 → 310
    YjeF_N; YjeF-related protein N-terminus
    pfam09532
    Location:54 → 155
    FDF; FDF domain
    pfam16598
    Location:1 → 52
    Edc3_linker; Linker region of enhancer of mRNA-decapping protein 3

  5. NM_025083.5 → NP_079359.2  enhancer of mRNA-decapping protein 3 isoform 1

    See identical proteins and their annotated locations for NP_079359.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) differs in the 5' UTR compared to variant 1. Variants 1-4 encode the same isoform (1).
    Source sequence(s)
    AC091230, BC011534
    Consensus CDS
    CCDS10267.1
    UniProtKB/Swiss-Prot
    B3KPH0, D3DW61, Q96F86, Q9H797
    Related
    ENSP00000320503.4, ENST00000315127.9
    Conserved Domains (4) summary
    cd01737
    Location:2 → 66
    LSm16_N; Like-Sm protein 16, N-terminal domain
    pfam03853
    Location:302 → 455
    YjeF_N; YjeF-related protein N-terminus
    pfam09532
    Location:199 → 300
    FDF; FDF domain
    pfam16598
    Location:104 → 197
    Edc3_linker; Linker region of enhancer of mRNA-decapping protein 3

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000015.10 Reference GRCh38.p14 Primary Assembly

    Range
    74630558..74696024 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_024450077.2 → XP_024305845.1  enhancer of mRNA-decapping protein 3 isoform X1

    UniProtKB/Swiss-Prot
    B3KPH0, D3DW61, Q96F86, Q9H797
    Conserved Domains (4) summary
    cd01737
    Location:2 → 66
    LSm16_N; Like-Sm protein 16, N-terminal domain
    pfam03853
    Location:302 → 455
    YjeF_N; YjeF-related protein N-terminus
    pfam09532
    Location:199 → 300
    FDF; FDF domain
    pfam16598
    Location:104 → 197
    Edc3_linker; Linker region of enhancer of mRNA-decapping protein 3

  2. XM_047433143.1 → XP_047289099.1  enhancer of mRNA-decapping protein 3 isoform X1

    UniProtKB/Swiss-Prot
    B3KPH0, D3DW61, Q96F86, Q9H797

  3. XM_024450079.2 → XP_024305847.1  enhancer of mRNA-decapping protein 3 isoform X1

    UniProtKB/Swiss-Prot
    B3KPH0, D3DW61, Q96F86, Q9H797
    Conserved Domains (4) summary
    cd01737
    Location:2 → 66
    LSm16_N; Like-Sm protein 16, N-terminal domain
    pfam03853
    Location:302 → 455
    YjeF_N; YjeF-related protein N-terminus
    pfam09532
    Location:199 → 300
    FDF; FDF domain
    pfam16598
    Location:104 → 197
    Edc3_linker; Linker region of enhancer of mRNA-decapping protein 3

  4. XM_011522092.4 → XP_011520394.1  enhancer of mRNA-decapping protein 3 isoform X2

    Conserved Domains (3) summary
    pfam03853
    Location:119 → 272
    YjeF_N; YjeF-related protein N-terminus
    pfam09532
    Location:16 → 117
    FDF; FDF domain
    pfam16598
    Location:1 → 14
    Edc3_linker; Linker region of enhancer of mRNA-decapping protein 3

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060939.1 Alternate T2T-CHM13v2.0

    Range
    72500459..72565921 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054378917.1 → XP_054234892.1  enhancer of mRNA-decapping protein 3 isoform X1

    UniProtKB/Swiss-Prot
    B3KPH0, D3DW61, Q96F86, Q9H797

  2. XM_054378918.1 → XP_054234893.1  enhancer of mRNA-decapping protein 3 isoform X1

    UniProtKB/Swiss-Prot
    B3KPH0, D3DW61, Q96F86, Q9H797

  3. XM_054378919.1 → XP_054234894.1  enhancer of mRNA-decapping protein 3 isoform X1

    UniProtKB/Swiss-Prot
    B3KPH0, D3DW61, Q96F86, Q9H797

  4. XM_054378920.1 → XP_054234895.1  enhancer of mRNA-decapping protein 3 isoform X2

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q96F86.1 GenPept UniProtKB/Swiss-Prot:Q96F86

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